Nucleic acid probes that recognize and report the presence of a specific nucleic acid sequence have been used to detect specific nucleic acids primarily in in vitro reactions. See, for example, U.S. Pat. No. 5,925,517, incorporated herein by reference. One type of probe is designed to have a hairpin-shaped structure, with a central stretch of nucleotides complementary to the target sequence, and termini comprising short mutually complementary sequences. See, for example, Tyagi and Kramer, Nature Biotechnology, 14, 303-308 (1996), incorporated herein by reference. One terminus of the stem-loop shaped probe is covalently bound to a fluorophore and the other to a quenching moiety. When in their native state with hybridized termini, the proximity of the fluorophore and the quencher is such that relatively little or essentially no fluorescence is produced. The stem-loop probe undergoes a conformational change when hybridized to its target nucleic acid that results in the detectable change in the production of fluorescence from the fluorophore. Researchers have used the hairpin-shaped probe to perform in-situ visualization of messenger RNA (Matsuo, 1998, Biochim. Biophys. Acta 1379:178-184) in living cells.